NM_006922.4(SCN3A):c.4121A>T (p.Asp1374Val) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 7, 2023
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000800894.9

Allele description [Variation Report for NM_006922.4(SCN3A):c.4121A>T (p.Asp1374Val)]

NM_006922.4(SCN3A):c.4121A>T (p.Asp1374Val)

Gene:

SCN3A:sodium voltage-gated channel alpha subunit 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_006922.4(SCN3A):c.4121A>T (p.Asp1374Val)

HGVS:

NC_000002.12:g.165097370T>A
NG_042289.1:g.111719A>T
NM_001081676.2:c.3974A>T
NM_001081677.2:c.3974A>T
NM_006922.4:c.4121A>TMANE SELECT
NP_001075145.1:p.Asp1325Val
NP_001075146.1:p.Asp1325Val
NP_008853.3:p.Asp1374Val
NC_000002.11:g.165953880T>A
NM_006922.3:c.4121A>T

Protein change:

D1325V

Links:

dbSNP: rs377507565

NCBI 1000 Genomes Browser:

rs377507565

Molecular consequence:

NM_001081676.2:c.3974A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001081677.2:c.3974A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006922.4:c.4121A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens spermatogenesis associated 33 (SPATA33), transcript variant 1, mRNA
Homo sapiens spermatogenesis associated 33 (SPATA33), transcript variant 1, mRNA
gi|1909429720|ref|NM_001271907.2|

Nucleotide
microplastic_lanthanum_biological_replicate_3
microplastic_lanthanum_biological_replicate_3

biosample
Model organism or animal sample from Pomoxis nigromaculatus
Model organism or animal sample from Pomoxis nigromaculatus

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000940637	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003930527	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 12, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000940637

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jul 7, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003930527

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 12, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000940637.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV003930527.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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